Biology subjects

Megremis, S.

Publications and source records attributed to Megremis, S..

6 recordsLinked to original sources

bioRxiv2026

Isolation and characterisation of Lytic Jumbo Klebsiella phage BMPCR_005026

Background: Klebsiella pneumoniae is a key causative agent of multidrug resistant nosocomial infections. Bacteriophages offer a promising alternative treatment, but the diversity of Klebsiella species requires the characterisation of a broad range of phages, particularly the poorly characterised jumbo phages. Materials and Methods: Phage BMCPR_005026 was isolated from sewage against Klebsiella pneumoniae. Whole genome sequencing, transmission electron microscopy and host range analysis against a diverse set of 40 clinically relevant Klebsiella strains were used to characterise the phage. Results: The virion had a myovirus morphology and genomic analysis placed it within an undefined family in Caudoviricetes where it forms a new species within the genus Alcyoneusvirus. BMCPR_005026 could form plaques on 3 of the 40 Klebsiella strains tested (7.5%) and formed halos. Conclusion: BMCPR_005026 represents a new species of phage within the genus Alcyoneusvirus with activity against 3 Klebsiella KL-types.

microbiology↗

bioRxiv2026

How many phage species remain undiscovered? Species sampling approaches to inform phage discovery

The emergence of antimicrobial resistant bacteria has been identified as one of the most serious public health and development threats for the near future. The use of bacteriophages (phages) is a promising solution for the sustainable control of these pathogens. Phages are natural viral predators of bacterial pathogens. However, due to the variability and adaptability of bacteria, developing effective and sustainable phage treatments requires drawing from a wide variety of different phage species. This study applies specialised mathematical and computational estimation approaches to the problem of sampling and discovering species of phages in microbiological communities. Our goal is to predict how many new phage species will be discovered in future samples based on species recorded in a phage sequence database for eight common bacterial hosts. While internal validation shows that current estimators yield low prediction errors for how many new species can be found when sampling more phages, these critically assume that the underlying mechanisms of phage sampling and database inclusion remain similar across time - an assumption put into question by our analysis for all but the host genus Mycobacterium. From this, we discuss how our results can still inform future sampling strategies - both through directly predicting the number of additional species, or by detecting changes in sampling and database inclusion. Our results have the potential to inform and optimise the hunt for and isolation of novel of phages from the the natural environment. HighlightsO_LISpecies abundance distribution of phages infecting seven of eight analysed host bacterial genera collected in phage databases changed significantly over time. C_LIO_LIMaintaining current sampling strategies for phages of host Mycobacteriut may lead to diminishing returns in the number of new phages found in additional samples. C_LIO_LIBoth non-parametric and parametric estimators of the numbers of unseen species show comparable, moderate errors when predicting a random subset from the remainder of hostspecific phage sets from the INPHARED database C_LI

genomics↗

bioRxiv2025

Rolling out plaque-2-sequence: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques

Rapid, accurate, and scalable sequencing of bacteriophage genomes is critical to advance phage therapy, build phage biobanks and understand phage genomic diversity. Current methods are based on sequencing and assembling complete bacteriophage genomes using short- or long-read technologies. However, current protocols require large DNA input and are cost prohibitive which limits their application to phage collections that typically are large and have low-biomass. In order to address this we have developed plaque-2-sequence, a robust and cost-effective workflow for high-throughput phage genome sequencing that will transform the speed and cost of attaining phage genomes. Plaque-2-sequence combines low-input transposase-based library preparation, amplification, nanopore sequencing and optimised assembly steps tailored to phage genomes. We applied the method to phages isolated on seven genetically diverse bacterial hosts; Escherichia, Pseudomonas, Synechococcus, Enterococcus, Klebsiella , Serratia and Enterobacter. High quality genome assemblies were validated using CheckV and benchmarking against previously sequenced phage isolates. Compared to standard Illumina sequencing, plaque-2-sequence offers [~]10-fold savings in sequencing price for individual labs. Furthermore, it substantially decreases the time required to produce a phage genome, once a plaque is obtained. Offering the ability to routinely obtain hundreds of phage genome sequences a week, with minimal hands-on time. Plaque-2-sequence enables systematic genomic characterisation of phage isolates, facilitating taxonomic classification, for the development of large scale phage biobanks. Impact StatementHere we have optimised a method for high-throughput sequencing of bacteriophage genomes from single plaques (plaque-2-sequence). We present a robust, high-throughput and cost-effective workflow. Plaque-2-sequence combines low-input transposase-based library preparation, amplification, nanopore sequencing and optimised assembly steps tailored to phage genomes. We demonstrate the scalability of this approach by sequencing over 100 phages from multiple bacterial hosts. This marks a step-change for the field, allowing phage genome sequencing to keep pace with phage isolation rates, and transforming how rapidly we can explore and understand phage genomic diversity.

microbiology↗

bioRxiv2023

Lysogeny destabilizes computationally simulated microbiomes

BackgroundThe Anna Karenina Principle predicts that stability in host-associated microbiomes correlates with health in the host. Microbiomes are ecosystems, and classical ecological theory suggests that predators impact ecosystem stability. Phages can act as predators on bacterial species in microbiomes. However, our ability to extrapolate results from existing ecological theory to phages and microbiomes is limited because some phages can stage lysogenic infections, a process with no precise analog in classical ecology. In lysogenic infections, so-called "temperate" phages integrate into the cells of their hosts where they can remain dormant as prophages for many generations. Prophages can later be induced by environmental conditions, whereupon they lyse their host cells and phage progeny are released. It has been suggested that prophages can act as biological timebombs that destabilize microbial ecosystems, but formal theory to support this hypothesis is lacking. ResultsWe studied the effects of temperate and virulent phages on diversity and stability in computationally simulated microbiomes. The presence of either phage type in a microbiome increased bacterial diversity. Bacterial populations were more likely to fluctuate over time when there were more temperate phages in the system. When microbiomes were disturbed from their steady states, both phage types affected return times, but in different ways. Bacterial species returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species. ConclusionsPhages shape the diversity and stability of microbiomes, and temperate and virulent phages impact microbiomes in different ways. A clear understanding of the effects of phage life cycles on microbiome dynamics is needed to predict the role of microbiome composition in host health, and for applications including phage therapy and microbiome transplants. The results we present here provide a theoretical foundation for this body of work.

ecology↗

bioRxiv2020

Bacteriophage deficiency characterizes respiratory virome dysbiosis in childhood asthma

Asthma development and persistence is tightly linked to respiratory viruses. Viral presence is usually interrogated with targeted approaches during periods of disease activity and/or infections, thus neglecting viral occurrence during steady states. We investigate the virome in the upper respiratory system of healthy and asthmatic preschool children during asymptomatic/non-infection periods using metagenomics. Children with asthma have a characteristically dysbiotic virome that correlates to disease severity and control. The major component of dysbiosis is bacteriophage deficiency, while eukaryotic viral presence is increased. At the metacommunity level, differential virus species co-occurrence patterns suggest a decrease of the microbiota community resilience in asthma. Viral dysbiosis is therefore a key characteristic of asthma pathophysiology.

microbiology↗

bioRxiv2020

Microbial and autoantibody immunogenic repertoires in TIF1γ autoantibody positive dermatomyositis

We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1{gamma} (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. Increased microbial diversity was observed in dermatomyositis. Viruses were over-represented and species of the Poxviridae family were significantly enriched. The autoantibodies identified recognised a large portion of the human proteome, including interferon regulated proteins; these proteins were clustered in specific biological processes. Apart from TRIM33, autoantibodies against eleven further TRIM proteins, including TRIM21, were identified. Some of these TRIM proteins shared epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a significant role in the pathogenesis of dermatomyositis.

immunology↗